Biocomputing: Structural bioinformatics and computational genomics
Jürgen Sühnel has retired as FLI Group Leader in June 2011. He is still affiliated with the institute as coordinator of JenAge.
We did research in the field of bioinformatics and computational biology with an emphasis on structural biology and computational genomics. In the structural biology field we have been interested in the identification and analysis of unusual motifs and interactions in three-dimensional structures of proteins and nucleic acids. Our research involved different techniques including quantum-chemical calculations, molecular dynamics simulations and structural bioinformatics approaches.
More specifically, we have worked
- water-mediated interactions in nucleic acid base pairs,
- the geometry and electronic structure of base tetrad motifs occurring in telomere structures, for example,
- C-H...O-, C-H...N- and C-H...PI interactions,
- the role of non-repetitive dipeptide motifs in proteins that correspond to transitions between different Ramachandran plot clusters.
Our computational genomics work was aimed at the development of tools for an accelerated and improved annotation and analysis of prokaryotic genomes. In addition, a new genome browser type that encodes the nucleic acid sequence by physico-chemical dinucleotide properties was developed. We also applied mathematical methods to microscopical, FISH (fluorescence in situ hybridization) and imaging techniques.
We have developed and are maintaining a variety of widely used databases and webtools as e.g.:
- JenaLib: The Jena Library of Biological Macromolecules
- The Jena3D Viewer
- JPGV: The Jena Prokaryotic Genome Viewer
- SGB: The Spirochetes Genome Browser
- XGB: The Xanthomonas Genome Browser
- engene: The Enterobacteria Genome Browser
- DiProDB: Dinucleotide Property Database
- DiProGB: The Dinucleotide Properties Genome Browser
- The RNA World Website
- The JCB Protein-Protein Interaction Website
The Sühnel Group was coordinating the Jena Centre for Bioinformatics - JCB between 2001 and 2007. Currently, Jürgen Sühnel is acting as the coordinator of The Jena Centre for Systems Biology of Ageing - JenAge.
With the Diekmann Lab and Platzer Lab.
- M. Meyer, Revotar Biopharmaceuticals, Hennigsdorf,
- C. Skerka and P. Zipfel, Hans Knöll Institute, Jena,
- A. Gutermann, Medigene, Martinsried,
- P. Dittrich, Jena University,
- M. Hausmann, Heidelberg University
- E.B. Pedersen, University of Southern Denmark, Odense